[gmx-developers] Re: [gmx-users] unexpexted stop of simulation

Bogdan Costescu bcostescu at gmail.com
Thu Nov 4 04:39:01 CET 2010

On Thu, Nov 4, 2010 at 1:08 AM, Roland Schulz <roland at utk.edu> wrote:
> BTW: Is it somehow possible to print the kernel error messages that are
> shown by dmesg to the user from within GROMACS? That would help the user to
> directly see the reason of the error. Thus I'm looking for a function
> similar to strerror but which returns the kernel message not just the
> message of the error code (which in this case was just "Input/Output
> errror".

Hi Roland!

In general, it's not possible to make a connection between a message
logged by the Linux kernel (which is then shown by dmesg or the system
logging) and a particular call to an I/O function. More specifically,
dmesg just dumps the kernel log buffer which, to my knowledge, doesn't
contain time information, so the last message in the buffer and the
last I/O operation cannot be correlated this way; the system logging
(syslogd and similar) attaches time information, but it's usually only
readable by root for security reasons - and even if it would be
readable by the GROMACS user, there is no way to uniquely associate an
entry in syslog with a particular I/O operation on a
multiuser/multitasking OS. It might be doable using a tracing
infrastructure in the kernel... but that's no longer generic.


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